Hello again!
I spoke too soon. I figured that the java.lang.NullPointerException was fixed because it didn't come up when I start fiji from the command line. I am now running ImageJ 1.47i; java 1.7.0_13 [64bit]. When I run a macro, I get this error:
gserver% fiji -Dplugins.dir=$FDIR -macro ./MontageMacro3.ijm -batch &
[1] 11974
gserver% java.lang.NullPointerException
at fiji.User_Plugins.runPlugIn(User_Plugins.java:142)
at fiji.User_Plugins.installScripts(User_Plugins.java:153)
at fiji.User_Plugins.run(User_Plugins.java:99)
at fiji.Main.setup(Main.java:331)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at ij.macro.Functions.call(Functions.java:3696)
at ij.macro.Functions.getStringFunction(Functions.java:262)
at ij.macro.Interpreter.getStringTerm(Interpreter.java:1220)
at ij.macro.Interpreter.getString(Interpreter.java:1199)
at ij.macro.Interpreter.doStatement(Interpreter.java:264)
at ij.macro.Interpreter.doStatements(Interpreter.java:207)
at ij.macro.Interpreter.run(Interpreter.java:104)
at ij.macro.Interpreter.run(Interpreter.java:74)
at ij.macro.Interpreter.run(Interpreter.java:85)
at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:105)
at ij.IJ.runMacro(IJ.java:104)
at ij.IJ.runMacro(IJ.java:93)
at ij.ImageJ.main(ImageJ.java:678)
at fiji.Main.main(Main.java:363)
Here is the Macro:
input = "/home/gserver/Pictures/Microscopy/08Feb13/ND_files/";
output = "/home/gserver/Pictures/Microscopy/08Feb13/processed/";
setBatchMode(true);
list = getFileList(input);
for (i = 0; i < list.length; i++)
action(input, output, list[i]);
setBatchMode(false);
function action(input, output, filename) {
open(input + filename);
run("RGB Color");
saveAs("Tiff", "/tmp/Z0.tif");
run("Z Project...", "start=1 stop=3 projection=[Max Intensity]");
run("Scale Bar...", "width=100 height=5 font=18 color=White background=None location=[Lower Right] bold");
run("Flatten");
saveAs("Tiff", "/tmp/fijitemp/A1.tif");
close();
close();
open("/tmp/Z0.tif");
run("Stack to Images");
run("Scale Bar...", "width=100 height=5 font=18 color=White background=None location=[Lower Right] bold");
run("Flatten");
saveAs("Tiff", "/tmp/fijitemp/A2.tif");
close();
close();
run("Scale Bar...", "width=100 height=5 font=18 color=White background=None location=[Lower Right] bold");
run("Flatten");
saveAs("Tiff", "/tmp/fijitemp/A3.tif");
close();
close();
run("Scale Bar...", "width=100 height=5 font=18 color=White background=None location=[Lower Right] bold");
run("Flatten");
saveAs("Tiff", "/tmp/fijitemp/A4.tif");
close();
close();
run("Image Sequence...", "open=/tmp/fijitemp/ number=4 starting=1 increment=1 scale=100 file=[] or=[] sort");
run("Make Montage...", "columns=2 rows=2 scale=0.50 first=1 last=4 increment=1 border=0 font=12");
saveAs("TIFF", output + filename);
close();
}
setBatchMode(false);
//setTool("angle");
I am automating the conversion of ND2 files from a Nikon microscope to montage tifs. Maybe the macro is calling a non-compatible plugin. Hopefully not bio-formats? Any help or information is greatly appreciated!! Thanks!
Matt
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html
Locked
